Castellano-Escuder, Pol, Derek K. Zachman, Kevin Han, and Matthey D. Hirschey. “GAUDI: interpretable multi-omics integration with UMAP embeddings and density-based clustering.” Nat Commun 16, no. 1 (July 1, 2025): 5771. https://doi.org/10.1038/s41467-025-60822-1.

Anderson, Kristin A., Beverly deSouza, Pol Castellano-Escuder, Zhihong Lin, Olga R. Ilkayeva, Michael J. Muehlbauer, Paul A. Grimsrud, and Matthew D. Hirschey. “SIRT4 Controls Macrophage Function and Wound Healing through Control of Protein Itaconylation in Mice.” BioRxiv, May 13, 2025. https://doi.org/10.1101/2025.05.12.653532.

Bonglack, Emmanuela N., Kaeden K. Hill, Ashley P. Barry, Alexandria Bartlett, Pol Castellano-Escuder, Matthew D. Hirschey, and Micah A. Luftig. “Fatty acid desaturases link cell metabolism pathways to promote proliferation of Epstein-Barr virus-infected B cells.” PLoS Pathog 21, no. 5 (May 2025): e1012685. https://doi.org/10.1371/journal.ppat.1012685.

Stewart, Amy E., Derek K. Zachman, Pol Castellano-Escuder, Lois M. Kelly, Ben Zolyomi, Michael D. I. Aiduk, Christopher D. Delaney, et al. “Pathway Coessentiality Mapping Reveals Complex II is Required for de novo Purine Biosynthesis in Acute Myeloid Leukemia.” BioRxiv, March 2, 2025. https://doi.org/10.1101/2025.02.26.640463.

Castellano-Escuder, Pol, Derek K. Zachman, Kevin Han, and Matthey D. Hirschey. “Interpretable multi-omics integration with UMAP embeddings and density-based clustering.” BioRxiv, October 11, 2024. https://doi.org/10.1101/2024.10.07.617035.

Keenan, E Keith, Akshay Bareja, Yannie Lam, Paul A. Grimsrud, and Matthew D. Hirschey. “Cysteine S-acetylation is a post-translational modification involved in metabolic regulation.,” May 21, 2024. https://doi.org/10.1101/2024.05.21.595030.

Sunassee, Enakshi D., Riley J. Deutsch, Victoria W. D’Agostino, Pol Castellano-Escuder, Elizabeth A. Siebeneck, Olga Ilkayeva, Brian T. Crouch, et al. “Optical imaging reveals chemotherapy-induced metabolic reprogramming of residual disease and recurrence.” Sci Adv 10, no. 14 (April 5, 2024): eadj7540. https://doi.org/10.1126/sciadv.adj7540.

Bonglack, Emmanuela, Kaeden Hill, Ashley Barry, Alexandria Bartlett, Pol Castellano-Escuder, Matthew Hirschey, and Micah Luftig. “Fatty acid desaturases link cell metabolism pathways to promote proliferation of Epstein-Barr virus-infected B cells.” BioRxiv, 2024. https://doi.org/10.1101/2024.10.21.619359.

Myakala, Komuraiah, Xiaoxin X. Wang, Nataliia V. Shults, Ewa Krawczyk, Bryce A. Jones, Xiaoping Yang, Avi Z. Rosenberg, et al. “NAD metabolism modulates inflammation and mitochondria function in diabetic kidney disease.” J Biol Chem 299, no. 8 (August 2023): 104975. https://doi.org/10.1016/j.jbc.2023.104975.

Madonna, Megan C., Joy E. Duer, Brock J. McKinney, Enakshi D. Sunassee, Brian T. Crouch, Olga Ilkayeva, Matthew D. Hirschey, James V. Alvarez, and Nirmala Ramanujam. “In vivo metabolic imaging identifies lipid vulnerability in a preclinical model of Her2+/Neu breast cancer residual disease and recurrence.” NPJ Breast Cancer 8, no. 1 (September 26, 2022): 111. https://doi.org/10.1038/s41523-022-00481-3.

Trub, Alec G., Gregory R. Wagner, Kristin A. Anderson, Scott B. Crown, Guo-Fang Zhang, J Will Thompson, Olga R. Ilkayeva, et al. “Statin therapy inhibits fatty acid synthase via dynamic protein modifications.” Nat Commun 13, no. 1 (May 10, 2022): 2542. https://doi.org/10.1038/s41467-022-30060-w.

Bhatt, Dhaval P., C Allie Mills, Kristin A. Anderson, Bárbara J. Henriques, Tânia G. Lucas, Sara Francisco, Juan Liu, et al. “Deglutarylation of glutaryl-CoA dehydrogenase by deacylating enzyme SIRT5 promotes lysine oxidation in mice.” J Biol Chem 298, no. 4 (April 2022): 101723. https://doi.org/10.1016/j.jbc.2022.101723.

Hershberger, Kathleen A., John P. Rooney, Elena A. Turner, Lauren J. Donoghue, Rakesh Bodhicharla, Laura L. Maurer, Ian T. Ryde, et al. “Early-life mitochondrial DNA damage results in lifelong deficits in energy production mediated by redox signaling in Caenorhabditis elegans.” Redox Biol 43 (July 2021): 102000. https://doi.org/10.1016/j.redox.2021.102000.

Keenan, E Keith, Derek K. Zachman, and Matthew D. Hirschey. “Discovering the landscape of protein modifications.” Molecular Cell 81, no. 9 (May 2021): 1868–78. https://doi.org/10.1016/j.molcel.2021.03.015.

Mills, Christine A., Xianxi Wang, Dhaval P. Bhatt, Paul A. Grimsrud, Jacob Peter Matson, Debojyoti Lahiri, Daniel J. Burke, Jeanette Gowen Cook, Matthew D. Hirschey, and Michael J. Emanuele. “Sirtuin 5 Is Regulated by the SCFCyclin F Ubiquitin Ligase and Is Involved in Cell Cycle Control.” Mol Cell Biol 41, no. 2 (January 25, 2021). https://doi.org/10.1128/MCB.00269-20.

Gonzalez-Hunt, Claudia P., Anthony L. Luz, Ian T. Ryde, Elena A. Turner, Olga R. Ilkayeva, Dhaval P. Bhatt, Matthew D. Hirschey, and Joel N. Meyer. “Multiple metabolic changes mediate the response of Caenorhabditis elegans to the complex I inhibitor rotenone.” Toxicology 447 (January 15, 2021): 152630. https://doi.org/10.1016/j.tox.2020.152630.

Madonna, Megan C., Joy E. Duer, Joyce V. Lee, Jeremy Williams, Baris Avsaroglu, Caigang Zhu, Riley Deutsch, et al. “In Vivo Optical Metabolic Imaging of Long-Chain Fatty Acid Uptake in Orthotopic Models of Triple-Negative Breast Cancer.” Cancers (Basel) 13, no. 1 (January 5, 2021). https://doi.org/10.3390/cancers13010148.

Trub, Alec, Greggory Wagner, Scott Crown, Guo-Fang Zhang, Will Thompson, Olga Ilkayeva, Robert Stevens, Paul Grimsrud, Donald Backos, and Matthew Hirschey. “Statin therapy inhibits fatty acid synthase via dynamic protein modifications.” Research Square, 2021. https://doi.org/10.21203/rs.3.rs-465103/v1.

Myakala, Komuraiah, Xiaoxin Wang, Nataliia Shults, Bryce Jones, Xiaoping Yang, Avi Rosenberg, Brandon Ginley, et al. “NAD metabolism modulates inflammation and mitochondria function in diabetic kidney disease.” BioRxiv, 2021. https://doi.org/10.1101/2021.12.05.471273.

Enriquez-Hesles, Elisa, Daniel L. Smith, Nazif Maqani, Margaret B. Wierman, Matthew D. Sutcliffe, Ryan D. Fine, Agata Kalita, et al. “A cell-nonautonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism.” J Biol Chem 296 (2021): 100125. https://doi.org/10.1074/jbc.RA120.015402.

Enriquez-Hesles, Elisa, Daniel L. Smith, Nazif Maqani, Margaret B. Wierman, Matthew D. Sutcliffe, Ryan D. Fine, Agata Kalita, et al. “A cell-nonautonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism.” J Biol Chem 296 (December 2, 2020): 100125. https://doi.org/10.1074/jbc.RA120.015402.

Huynh, Frank K., Brett S. Peterson, Kristin A. Anderson, Zhihong Lin, Aeowynn J. Coakley, Fiara M. S. Llaguno, Thi-Tina N. Nguyen, et al. “β-Cell-specific ablation of sirtuin 4 does not affect nutrient-stimulated insulin secretion in mice.” Am J Physiol Endocrinol Metab 319, no. 4 (October 1, 2020): E805–13. https://doi.org/10.1152/ajpendo.00170.2020.

Hirschey, Matthew. “Lab life - rebuild it better after coronavirus lockdowns ease.” Nature 582, no. 7811 (June 2020): 184. https://doi.org/10.1038/d41586-020-01708-8.

Fox, Douglas B., Nina Marie G. Garcia, Brock J. McKinney, Ryan Lupo, Laura C. Noteware, Rachel Newcomb, Juan Liu, Jason W. Locasale, Matthew D. Hirschey, and James V. Alvarez. “NRF2 activation promotes the recurrence of dormant tumour cells through regulation of redox and nucleotide metabolism.” Nat Metab 2, no. 4 (April 2020): 318–34. https://doi.org/10.1038/s42255-020-0191-z.

Madonna, Megan, Joy Duer, Joyce Lee, Jeremy Williams, Baris Avsaroglu, Caigang Zhu, Riley Deutsch, et al. “In vivo optical metabolic imaging of long-chain fatty acid uptake in orthotopic models of triple negative breast cancer,” 2020. https://doi.org/10.1101/2020.11.02.365288.

Rooney, John, Kathleen Hershberger, Elena Turner, Lauren Donoghue, Laura Maurer, Ian Ryde, Jina Kim, et al. “Early-life mitochondrial DNA damage results in lifelong deficits in energy production mediated by redox signaling inCaenorhabditis elegans.” BioRxiv, 2020. https://doi.org/10.1101/2020.11.25.398164.

Bhatt, Dhaval, Allie Mills, Kristin Anderson, Bárbara Henriques, Tânia Lucas, Sara Francisco, Juan Liu, et al. “Deglutarylation of GCDH by SIRT5 controls lysine metabolism in mice.” BioRxiv, 2020. https://doi.org/10.1101/2020.06.28.176677.

Enriquez-Hesles, Elisa, Daniel Smith, Nazif Maqani, Margaret Wierman, Matthew Sutcliffe, Ryan Fine, Agata Kalita, et al. “A cell non-autonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism.” BioRxiv, 2020. https://doi.org/10.1101/2020.07.13.200493.

Hirschey, Matthew. “Making data-driven hypotheses for gene functions by integrating dependency, expression, and literature data,” 2020. https://doi.org/10.1101/2020.07.17.208751.

Naiman, Shoshana, Frank K. Huynh, Reuven Gil, Yair Glick, Yael Shahar, Noga Touitou, Liat Nahum, et al. “SIRT6 Promotes Hepatic Beta-Oxidation via Activation of PPARα.” Cell Rep 29, no. 12 (December 17, 2019): 4127-4143.e8. https://doi.org/10.1016/j.celrep.2019.11.067.

Assiri, Mohammed A., Hadi R. Ali, John O. Marentette, Youngho Yun, Juan Liu, Matthew D. Hirschey, Laura M. Saba, Peter S. Harris, and Kristofer S. Fritz. “Investigating RNA expression profiles altered by nicotinamide mononucleotide therapy in a chronic model of alcoholic liver disease.” Hum Genomics 13, no. 1 (December 10, 2019): 65. https://doi.org/10.1186/s40246-019-0251-1.

Ericksen, Russell E., Siew Lan Lim, Eoin McDonnell, Wai Ho Shuen, Maya Vadiveloo, Phillip J. White, Zhaobing Ding, et al. “Loss of BCAA Catabolism during Carcinogenesis Enhances mTORC1 Activity and Promotes Tumor Development and Progression.” Cell Metab 29, no. 5 (May 7, 2019): 1151-1165.e6. https://doi.org/10.1016/j.cmet.2018.12.020.

Ali, Hadi R., Mohammed A. Assiri, Peter S. Harris, Cole R. Michel, Youngho Yun, John O. Marentette, Frank K. Huynh, et al. “Quantifying Competition among Mitochondrial Protein Acylation Events Induced by Ethanol Metabolism.” J Proteome Res 18, no. 4 (April 5, 2019): 1513–31. https://doi.org/10.1021/acs.jproteome.8b00800.

Nicholatos, Justin W., Timothy M. Robinette, Saurabh V. P. Tata, Jennifer D. Yordy, Adam B. Francisco, Michael Platov, Tiffany K. Yeh, et al. “Cellular energetics and mitochondrial uncoupling in canine aging.” Geroscience 41, no. 2 (April 2019): 229–42. https://doi.org/10.1007/s11357-019-00062-6.

Fisher-Wellman, Kelsey H., James A. Draper, Michael T. Davidson, Ashley S. Williams, Tara M. Narowski, Dorothy H. Slentz, Olga R. Ilkayeva, et al. “Respiratory Phenomics across Multiple Models of Protein Hyperacylation in Cardiac Mitochondria Reveals a Marginal Impact on Bioenergetics.” Cell Rep 26, no. 6 (February 5, 2019): 1557-1572.e8. https://doi.org/10.1016/j.celrep.2019.01.057.

Fox, Douglas, Ryan Lupo, Laura Noteware, Rachel Newcomb, Juan Liu, Jason Locasale, Matthew Hirschey, and James Alvarez. “NRF2-dependent metabolic reprogramming is required for tumor recurrence following oncogene inhibition.” BioRxiv, 2019. https://doi.org/10.1101/513994.

Mills, Christine A., Alec G. Trub, and Matthew D. Hirschey. “Sensing Mitochondrial Acetyl-CoA to Tune Respiration.” Trends Endocrinol Metab 30, no. 1 (January 2019): 1–3. https://doi.org/10.1016/j.tem.2018.10.003.

Hershberger, Kathleen A., Dennis M. Abraham, Juan Liu, Jason W. Locasale, Paul A. Grimsrud, and Matthew D. Hirschey. “Ablation of Sirtuin5 in the postnatal mouse heart results in protein succinylation and normal survival in response to chronic pressure overload.” J Biol Chem 293, no. 27 (July 6, 2018): 10630–45. https://doi.org/10.1074/jbc.RA118.002187.

Peterson, Brett S., Jonathan E. Campbell, Olga Ilkayeva, Paul A. Grimsrud, Matthew D. Hirschey, and Christopher B. Newgard. “Remodeling of the Acetylproteome by SIRT3 Manipulation Fails to Affect Insulin Secretion or β Cell Metabolism in the Absence of Overnutrition.” Cell Rep 24, no. 1 (July 3, 2018): 209-223.e6. https://doi.org/10.1016/j.celrep.2018.05.088.

Trub, Alec G., and Matthew D. Hirschey. “Reactive Acyl-CoA Species Modify Proteins and Induce Carbon Stress.” Trends Biochem Sci 43, no. 5 (May 2018): 369–79. https://doi.org/10.1016/j.tibs.2018.02.002.

Hershberger, K. A., and M. D. Hirschey. “Reactive Acyl-CoA Species and Deacylation by the Mitochondrial Sirtuins.” In Introductory Review on Sirtuins in Biology Aging and Disease, 83–93, 2018. https://doi.org/10.1016/B978-0-12-813499-3.00007-1.

Hu, Yue, Ivana Semova, Xiaowei Sun, Hong Kang, Satyapal Chahar, Anthony N. Hollenberg, David Masson, Matthew D. Hirschey, Ji Miao, and Sudha B. Biddinger. “Fructose and glucose can regulate mammalian target of rapamycin complex 1 and lipogenic gene expression via distinct pathways.” J Biol Chem 293, no. 6 (February 9, 2018): 2006–14. https://doi.org/10.1074/jbc.M117.782557.

Huynh, Frank K., Xiaoke Hu, Zhihong Lin, James D. Johnson, and Matthew D. Hirschey. “Loss of sirtuin 4 leads to elevated glucose- and leucine-stimulated insulin levels and accelerated age-induced insulin resistance in multiple murine genetic backgrounds.” J Inherit Metab Dis 41, no. 1 (January 2018): 59–72. https://doi.org/10.1007/s10545-017-0069-8.

Weir, Heather J., Pallas Yao, Frank K. Huynh, Caroline C. Escoubas, Renata L. Goncalves, Kristopher Burkewitz, Raymond Laboy, Matthew D. Hirschey, and William B. Mair. “Dietary Restriction and AMPK Increase Lifespan via Mitochondrial Network and Peroxisome Remodeling.” Cell Metab 26, no. 6 (December 5, 2017): 884-896.e5. https://doi.org/10.1016/j.cmet.2017.09.024.

Anderson, Kristin A., Andreas S. Madsen, Christian A. Olsen, and Matthew D. Hirschey. “Metabolic control by sirtuins and other enzymes that sense NAD+, NADH, or their ratio.” Biochim Biophys Acta Bioenerg 1858, no. 12 (December 2017): 991–98. https://doi.org/10.1016/j.bbabio.2017.09.005.

Hershberger, Kathleen A., Dennis M. Abraham, Angelical S. Martin, Lan Mao, Juan Liu, Hongbo Gu, Jason W. Locasale, and Matthew D. Hirschey. “Sirtuin 5 is required for mouse survival in response to cardiac pressure overload.” J Biol Chem 292, no. 48 (December 1, 2017): 19767–81. https://doi.org/10.1074/jbc.M117.809897.

Rajabi, Nima, Marina Auth, Kathrin R. Troelsen, Martin Pannek, Dhaval P. Bhatt, Martin Fontenas, Matthew D. Hirschey, Clemens Steegborn, Andreas S. Madsen, and Christian A. Olsen. “Mechanism-Based Inhibitors of the Human Sirtuin 5 Deacylase: Structure-Activity Relationship, Biostructural, and Kinetic Insight.” Angew Chem Int Ed Engl 56, no. 47 (November 20, 2017): 14836–41. https://doi.org/10.1002/anie.201709050.

Hibshman, Jonathan D., Alexander E. Doan, Brad T. Moore, Rebecca Ew Kaplan, Anthony Hung, Amy K. Webster, Dhaval P. Bhatt, Rojin Chitrakar, Matthew D. Hirschey, and L Ryan Baugh. “daf-16/FoxO promotes gluconeogenesis and trehalose synthesis during starvation to support survival.” Elife 6 (October 24, 2017). https://doi.org/10.7554/eLife.30057.

Assiri, Mohammed A., Samantha R. Roy, Peter S. Harris, Hadi Ali, Yongliang Liang, Colin T. Shearn, David J. Orlicky, et al. “Chronic Ethanol Metabolism Inhibits Hepatic Mitochondrial Superoxide Dismutase via Lysine Acetylation.” Alcohol Clin Exp Res 41, no. 10 (October 2017): 1705–14. https://doi.org/10.1111/acer.13473.

Martin, Angelical S., Dennis M. Abraham, Kathleen A. Hershberger, Dhaval P. Bhatt, Lan Mao, Huaxia Cui, Juan Liu, et al. “Nicotinamide mononucleotide requires SIRT3 to improve cardiac function and bioenergetics in a Friedreich's ataxia cardiomyopathy model.” JCI Insight 2, no. 14 (July 20, 2017). https://doi.org/10.1172/jci.insight.93885.

Wagner, Gregory R., Dhaval P. Bhatt, Thomas M. O’Connell, J Will Thompson, Laura G. Dubois, Donald S. Backos, Hao Yang, et al. “A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation.” Cell Metab 25, no. 4 (April 4, 2017): 823-837.e8. https://doi.org/10.1016/j.cmet.2017.03.006.

Anderson, Kristin A., Frank K. Huynh, Kelsey Fisher-Wellman, J Darren Stuart, Brett S. Peterson, Jonathan D. Douros, Gregory R. Wagner, et al. “SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion.” Cell Metab 25, no. 4 (April 4, 2017): 838-855.e15. https://doi.org/10.1016/j.cmet.2017.03.003.

Hirschey, Matthew. “Epigenetic Control of Gene Expression by Lipid Metabolism.” In FASEB JOURNAL, Vol. 31. FEDERATION AMER SOC EXP BIOL, 2017.

Hershberger, Kathleen A., Angelical S. Martin, and Matthew D. Hirschey. “Role of NAD+ and mitochondrial sirtuins in cardiac and renal diseases.” Nat Rev Nephrol 13, no. 4 (April 2017): 213–25. https://doi.org/10.1038/nrneph.2017.5.

Wagner, Gregory R., and Matthew D. Hirschey. “A Prob(e)able Route to Lysine Acylation.” Cell Chem Biol 24, no. 2 (February 16, 2017): 126–28. https://doi.org/10.1016/j.chembiol.2017.01.011.

Stram, Amanda R., Gregory R. Wagner, Brian D. Fogler, P Melanie Pride, Matthew D. Hirschey, and R Mark Payne. “Progressive mitochondrial protein lysine acetylation and heart failure in a model of Friedreich's ataxia cardiomyopathy.” PLoS One 12, no. 5 (2017): e0178354. https://doi.org/10.1371/journal.pone.0178354.

Zhang, Zhiquan, Qing Ma, Alina Nicoara, Quintin Quinones, Matthew Hirschey, and Mihai V. Podgoreanu. “Sex-Specific Cardioprotective Effects of Annexin A1 Peptide Mimetic Involve the Sirtuin 3 Signaling Pathway.” In CIRCULATION, Vol. 134. LIPPINCOTT WILLIAMS & WILKINS, 2016.

Luz, Anthony T., Tewodros R. Godebo, Dhaval P. Bhatt, Olga R. Ilkayeva, Laura L. Maurer, Matthew D. Hirschey, and Joel N. Meyer. “Arsenite Uncouples Mitochondrial Respiration and Induces a Warburg-Like Effect in Caenorhabditis elegans.” Toxicol Sci 154, no. 1 (November 2016): 195. https://doi.org/10.1093/toxsci/kfw185.

McDonnell, Eoin, Scott B. Crown, Douglas B. Fox, Betül Kitir, Olga R. Ilkayeva, Christian A. Olsen, Paul A. Grimsrud, and Matthew D. Hirschey. “Lipids Reprogram Metabolism to Become a Major Carbon Source for Histone Acetylation.” Cell Rep 17, no. 6 (November 1, 2016): 1463–72. https://doi.org/10.1016/j.celrep.2016.10.012.

Luz, Anthony L., Tewodros R. Godebo, Dhaval P. Bhatt, Olga R. Ilkayeva, Laura L. Maurer, Matthew D. Hirschey, and Joel N. Meyer. “From the Cover: Arsenite Uncouples Mitochondrial Respiration and Induces a Warburg-like Effect in Caenorhabditis elegans.” Toxicol Sci 152, no. 2 (August 2016): 349–62. https://doi.org/10.1093/toxsci/kfw093.

Luz, Anthony L., Cristina Lagido, Matthew D. Hirschey, and Joel N. Meyer. “In Vivo Determination of Mitochondrial Function Using Luciferase-Expressing Caenorhabditis elegans: Contribution of Oxidative Phosphorylation, Glycolysis, and Fatty Acid Oxidation to Toxicant-Induced Dysfunction.” Curr Protoc Toxicol 69 (August 1, 2016): 25.8.1-25.8.22. https://doi.org/10.1002/cptx.10.

Quinones, Quintin J., Zhiquan Zhang, Qing Ma, Michael P. Smith, Erik Soderblom, M Arthur Moseley, James Bain, et al. “Proteomic Profiling Reveals Adaptive Responses to Surgical Myocardial Ischemia-Reperfusion in Hibernating Arctic Ground Squirrels Compared to Rats.” Anesthesiology 124, no. 6 (June 2016): 1296–1310. https://doi.org/10.1097/ALN.0000000000001113.

Madsen, Andreas S., Christian Andersen, Mohammad Daoud, Kristin A. Anderson, Jonas S. Laursen, Saswati Chakladar, Frank K. Huynh, et al. “Investigating the Sensitivity of NAD+-dependent Sirtuin Deacylation Activities to NADH.” J Biol Chem 291, no. 13 (March 25, 2016): 7128–41. https://doi.org/10.1074/jbc.M115.668699.

Hirschey, Matthew D., Ralph J. DeBerardinis, Anna Mae E. Diehl, Janice E. Drew, Christian Frezza, Michelle F. Green, Lee W. Jones, et al. “Dysregulated metabolism contributes to oncogenesis.” Semin Cancer Biol 35 Suppl (December 2015): S129–50. https://doi.org/10.1016/j.semcancer.2015.10.002.

Block, Keith I., Charlotte Gyllenhaal, Leroy Lowe, Amedeo Amedei, ARM Ruhul Amin, Amr Amin, Katia Aquilano, et al. “Designing a broad-spectrum integrative approach for cancer prevention and treatment.” Semin Cancer Biol 35 Suppl, no. Suppl (December 2015): S276–304. https://doi.org/10.1016/j.semcancer.2015.09.007.

Huynh, F. K., E. Mcdonnell, K. A. Anderson, and M. D. Hirschey. “Sirtuins.” In Signaling Pathways in Liver Diseases Third Edition, 374–84, 2015. https://doi.org/10.1002/9781118663387.ch27.

Otsubo, Chikara, Sivakama Bharathi, Radha Uppala, Olga R. Ilkayeva, Dongning Wang, Kevin McHugh, Ye Zou, et al. “Long-chain Acylcarnitines Reduce Lung Function by Inhibiting Pulmonary Surfactant.” J Biol Chem 290, no. 39 (September 25, 2015): 23897–904. https://doi.org/10.1074/jbc.M115.655837.

McDonnell, Eoin, Brett S. Peterson, Howard M. Bomze, and Matthew D. Hirschey. “SIRT3 regulates progression and development of diseases of aging.” Trends Endocrinol Metab 26, no. 9 (September 2015): 486–92. https://doi.org/10.1016/j.tem.2015.06.001.

Hirschey, Matthew D., and Yingming Zhao. “Metabolic Regulation by Lysine Malonylation, Succinylation, and Glutarylation.” Mol Cell Proteomics 14, no. 9 (September 2015): 2308–15. https://doi.org/10.1074/mcp.R114.046664.

Huynh, Frank K., Deborah M. Muoio, and Matthew D. Hirschey. “SIRT3 Directs Carbon Traffic in Muscle to Promote Glucose Control.” Diabetes 64, no. 9 (September 2015): 3058–60. https://doi.org/10.2337/db15-0709.

Henriques, B. J., K. A. Anderson, M. D. Hirschey, and C. M. Gomes. “Regulation of mitochondria beta oxidation by non-enzymatic post-translational modifications.” In FEBS JOURNAL, 282:342–342. WILEY-BLACKWELL, 2015.

Liu, Xiaojing, Sushabhan Sadhukhan, Shengyi Sun, Gregory R. Wagner, Matthew D. Hirschey, Ling Qi, Hening Lin, and Jason W. Locasale. “High-Resolution Metabolomics with Acyl-CoA Profiling Reveals Widespread Remodeling in Response to Diet.” Mol Cell Proteomics 14, no. 6 (June 2015): 1489–1500. https://doi.org/10.1074/mcp.M114.044859.

Glass, O. K., B. A. Inman, G. Broadwater, K. S. Courneya, J. R. Mackey, S. Goruk, E. R. Nelson, et al. “Effect of aerobic training on the host systemic milieu in patients with solid tumours: An exploratory correlative study.” British Journal of Cancer 112, no. 5 (March 3, 2015): 825–31. https://doi.org/10.1038/bjc.2014.662.

Glass, O. K., B. A. Inman, G. Broadwater, K. S. Courneya, J. R. Mackey, S. Goruk, E. R. Nelson, et al. “Effect of aerobic training on the host systemic milieu in patients with solid tumours: an exploratory correlative study.” Br J Cancer 112, no. 5 (March 3, 2015): 825–31. https://doi.org/10.1038/bjc.2014.662.

Burkewitz, Kristopher, Ianessa Morantte, Heather J. M. Weir, Robin Yeo, Yue Zhang, Frank K. Huynh, Olga R. Ilkayeva, Matthew D. Hirschey, Ana R. Grant, and William B. Mair. “Neuronal CRTC-1 governs systemic mitochondrial metabolism and lifespan via a catecholamine signal.” Cell 160, no. 5 (February 26, 2015): 842–55. https://doi.org/10.1016/j.cell.2015.02.004.

Shaughnessy, Daniel T., Kimberly McAllister, Leroy Worth, Astrid C. Haugen, Joel N. Meyer, Frederick E. Domann, Bennett Van Houten, et al. “Mitochondria, energetics, epigenetics, and cellular responses to stress.” Environ Health Perspect 122, no. 12 (December 2014): 1271–78. https://doi.org/10.1289/ehp.1408418.

Moffat, Cynthia, Lavesh Bhatia, Teresa Nguyen, Peter Lynch, Miao Wang, Dongning Wang, Olga R. Ilkayeva, et al. “Acyl-CoA thioesterase-2 facilitates mitochondrial fatty acid oxidation in the liver.” J Lipid Res 55, no. 12 (December 2014): 2458–70. https://doi.org/10.1194/jlr.M046961.

Anderson, Kristin A., Michelle F. Green, Frank K. Huynh, Gregory R. Wagner, and Matthew D. Hirschey. “SnapShot: Mammalian Sirtuins.” Cell 159, no. 4 (November 6, 2014): 956-956.e1. https://doi.org/10.1016/j.cell.2014.10.045.

Huynh, Frank K., and Matthew D. Hirschey. “Loss of Sirtuin 4 Leads to Insulin Resistance in Mice.” ENDOCRINE REVIEWS 35, no. 3 (June 1, 2014).

Wagner, Gregory R., and Matthew D. Hirschey. “Nonenzymatic protein acylation as a carbon stress regulated by sirtuin deacylases.” Mol Cell 54, no. 1 (April 10, 2014): 5–16. https://doi.org/10.1016/j.molcel.2014.03.027.

Tan, Minjia, Chao Peng, Kristin A. Anderson, Peter Chhoy, Zhongyu Xie, Lunzhi Dai, Jeongsoon Park, et al. “Lysine glutarylation is a protein posttranslational modification regulated by SIRT5.” Cell Metab 19, no. 4 (April 1, 2014): 605–17. https://doi.org/10.1016/j.cmet.2014.03.014.

Huynh, Frank K., Michelle F. Green, Timothy R. Koves, and Matthew D. Hirschey. “Measurement of fatty acid oxidation rates in animal tissues and cell lines.” Methods Enzymol 542 (2014): 391–405. https://doi.org/10.1016/B978-0-12-416618-9.00020-0.

Schechter, Matthew A., Michael K. H. Hsieh, Linda W. Njoroge, J Will Thompson, Erik J. Soderblom, Bryan J. Feger, Constantine D. Troupes, et al. “Phosphoproteomic profiling of human myocardial tissues distinguishes ischemic from non-ischemic end stage heart failure.” PLoS One 9, no. 8 (2014): e104157. https://doi.org/10.1371/journal.pone.0104157.

Hirschey, Matthew. “Protein Acylation Regulates Metabolism.” In Biophysical Journal, 106:4a-4a. Elsevier BV, 2014. https://doi.org/10.1016/j.bpj.2013.11.053.

Bharathi, Sivakama S., Yuxun Zhang, Al-Walid Mohsen, Radha Uppala, Manimalha Balasubramani, Emanuel Schreiber, Guy Uechi, et al. “Sirtuin 3 (SIRT3) protein regulates long-chain acyl-CoA dehydrogenase by deacetylating conserved lysines near the active site.” J Biol Chem 288, no. 47 (November 22, 2013): 33837–47. https://doi.org/10.1074/jbc.M113.510354.

Hirschey, M. D. “Preface.” Methods in Molecular Biology 1077 (September 20, 2013).

Anderson, Kristin A., Dongning Wang, and Matthew D. Hirschey. “HINT2 and fatty liver disease: mitochondrial protein hyperacetylation gives a hint?” Hepatology 57, no. 5 (May 2013): 1681–83. https://doi.org/10.1002/hep.26085.

Huynh, Frank K., Kathleen A. Hershberger, and Matthew D. Hirschey. “Targeting sirtuins for the treatment of diabetes.” Diabetes Manag (Lond) 3, no. 3 (May 1, 2013): 245–57. https://doi.org/10.2217/dmt.13.6.

Merksamer, Philip I., Yufei Liu, Wenjuan He, Matthew D. Hirschey, Danica Chen, and Eric Verdin. “The sirtuins, oxidative stress and aging: an emerging link.” Aging (Albany NY) 5, no. 3 (March 2013): 144–50. https://doi.org/10.18632/aging.100544.

Green, Michelle F., and Matthew D. Hirschey. “SIRT3 weighs heavily in the metabolic balance: a new role for SIRT3 in metabolic syndrome.” J Gerontol A Biol Sci Med Sci 68, no. 2 (February 2013): 105–7. https://doi.org/10.1093/gerona/gls132.

Gut, Philipp, Bernat Baeza-Raja, Olov Andersson, Laura Hasenkamp, Joseph Hsiao, Daniel Hesselson, Katerina Akassoglou, Eric Verdin, Matthew D. Hirschey, and Didier Y. R. Stainier. “Whole-organism screening for gluconeogenesis identifies activators of fasting metabolism.” Nat Chem Biol 9, no. 2 (February 2013): 97–104. https://doi.org/10.1038/nchembio.1136.

Shimazu, Tadahiro, Matthew D. Hirschey, John Newman, Wenjuan He, Kotaro Shirakawa, Natacha Le Moan, Carrie A. Grueter, et al. “Suppression of oxidative stress by β-hydroxybutyrate, an endogenous histone deacetylase inhibitor.” Science 339, no. 6116 (January 11, 2013): 211–14. https://doi.org/10.1126/science.1227166.

Hershberger, Kathleen A., Jonathan Motley, Matthew D. Hirschey, and Kristin A. Anderson. “Generating mammalian sirtuin tools for protein-interaction analysis.” Methods Mol Biol 1077 (2013): 69–78. https://doi.org/10.1007/978-1-62703-637-5_5.

Wang, Dongning, Michelle F. Green, Eoin McDonnell, and Matthew D. Hirschey. “Oxygen flux analysis to understand the biological function of sirtuins.” Methods Mol Biol 1077 (2013): 241–58. https://doi.org/10.1007/978-1-62703-637-5_16.

Gut, P., B. Baeza-Raja, O. Andersson, L. Hasenkamp, J. Hsiao, D. Hesselson, K. Akassoglou, E. Verdin, M. D. Hirschey, and D. Y. R. Stainier. “Whole-organism screening for gluconeogenesis identifies activators of fasting metabolism.” Nature Chemical Biology 9, no. 2 (2013): 97–104. https://doi.org/10.1038/nchembio.1136.

Fritz, Kristofer S., Michelle F. Green, Dennis R. Petersen, and Matthew D. Hirschey. “Ethanol metabolism modifies hepatic protein acylation in mice.” PLoS One 8, no. 9 (2013): e75868. https://doi.org/10.1371/journal.pone.0075868.

Haas, Joel T., Ji Miao, Dipanjan Chanda, Yanning Wang, Enpeng Zhao, Mary E. Haas, Matthew Hirschey, et al. “Hepatic insulin signaling is required for obesity-dependent expression of SREBP-1c mRNA but not for feeding-dependent expression.” Cell Metab 15, no. 6 (June 6, 2012): 873–84. https://doi.org/10.1016/j.cmet.2012.05.002.

Fritz, Kristofer S., James J. Galligan, Matthew D. Hirschey, Eric Verdin, and Dennis R. Petersen. “Mitochondrial acetylome analysis in a mouse model of alcohol-induced liver injury utilizing SIRT3 knockout mice.” J Proteome Res 11, no. 3 (March 2, 2012): 1633–43. https://doi.org/10.1021/pr2008384.

Streeper, Ryan S., Carrie A. Grueter, Nathan Salomonis, Sylvaine Cases, Malin C. Levin, Suneil K. Koliwad, Ping Zhou, Mattew D. Hirschey, Eric Verdin, and Robert V. Farese. “Deficiency of the lipid synthesis enzyme, DGAT1, extends longevity in mice.” Aging (Albany NY) 4, no. 1 (January 2012): 13–27. https://doi.org/10.18632/aging.100424.

Anderson, Kristin A., and Matthew D. Hirschey. “Mitochondrial protein acetylation regulates metabolism.” Essays Biochem 52 (2012): 23–35. https://doi.org/10.1042/bse0520023.

Hirschey, Matthew D. “Old enzymes, new tricks: sirtuins are NAD(+)-dependent de-acylases.” Cell Metab 14, no. 6 (December 7, 2011): 718–19. https://doi.org/10.1016/j.cmet.2011.10.006.

Fritz, Kristofer S., James J. Galligan, Matthew D. Hirschey, Eric Verdin, and Dennis R. Petersen. “Mitochondrial Acetylomic Analysis in a Mouse Model of Alcohol-Induced Liver Injury Utilizing SIRT3 Knockout Mice.” Free Radical Biology and Medicine 51 (November 2011): S19–20. https://doi.org/10.1016/j.freeradbiomed.2011.10.044.

Hirschey, Matthew D., Tadahiro Shimazu, Enxuan Jing, Carrie A. Grueter, Amy M. Collins, Bradley Aouizerat, Alena Stančáková, et al. “SIRT3 deficiency and mitochondrial protein hyperacetylation accelerate the development of the metabolic syndrome.” Mol Cell 44, no. 2 (October 21, 2011): 177–90. https://doi.org/10.1016/j.molcel.2011.07.019.

Jing, Enxuan, Brice Emanuelli, Matthew D. Hirschey, Jeremie Boucher, Kevin Y. Lee, David Lombard, Eric M. Verdin, and C Ronald Kahn. “Sirtuin-3 (Sirt3) regulates skeletal muscle metabolism and insulin signaling via altered mitochondrial oxidation and reactive oxygen species production.” Proc Natl Acad Sci U S A 108, no. 35 (August 30, 2011): 14608–13. https://doi.org/10.1073/pnas.1111308108.

Hirschey, Matthew D., Tadahiro Shimazu, John A. Capra, Katherine S. Pollard, and Eric Verdin. “SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2.” Aging (Albany NY) 3, no. 6 (June 2011): 635–42. https://doi.org/10.18632/aging.100339.

Hirschey, M. D., T. Shimazu, J. -. Y. Huang, B. Schwer, and E. Verdin. “SIRT3 regulates mitochondrial protein acetylation and intermediary metabolism.” Cold Spring Harb Symp Quant Biol 76 (2011): 267–77. https://doi.org/10.1101/sqb.2011.76.010850.

Verdin, Eric, Matthew D. Hirschey, Lydia W. S. Finley, and Marcia C. Haigis. “Sirtuin regulation of mitochondria: energy production, apoptosis, and signaling.” Trends Biochem Sci 35, no. 12 (December 2010): 669–75. https://doi.org/10.1016/j.tibs.2010.07.003.

Qiu, Xiaolei, Katharine Brown, Matthew D. Hirschey, Eric Verdin, and Danica Chen. “Calorie restriction reduces oxidative stress by SIRT3-mediated SOD2 activation.” Cell Metab 12, no. 6 (December 1, 2010): 662–67. https://doi.org/10.1016/j.cmet.2010.11.015.

Shimazu, Tadahiro, Matthew D. Hirschey, Lan Hua, Kristin E. Dittenhafer-Reed, Bjoern Schwer, David B. Lombard, Yu Li, et al. “SIRT3 deacetylates mitochondrial 3-hydroxy-3-methylglutaryl CoA synthase 2 and regulates ketone body production.” Cell Metab 12, no. 6 (December 1, 2010): 654–61. https://doi.org/10.1016/j.cmet.2010.11.003.

Huang, Jing-Yi, Matthew D. Hirschey, Tadahiro Shimazu, Linh Ho, and Eric Verdin. “Mitochondrial sirtuins.” Biochim Biophys Acta 1804, no. 8 (August 2010): 1645–51. https://doi.org/10.1016/j.bbapap.2009.12.021.

Hirschey, Matthew D., and Eric Verdin. “Measuring fatty acid oxidation in tissue homogenates.” Protocol Exchange, April 15, 2010. https://doi.org/10.1038/nprot.2010.92.

Hirschey, Matthew D., Tadahiro Shimazu, Eric Goetzman, Enxuan Jing, Bjoern Schwer, David B. Lombard, Carrie A. Grueter, et al. “SIRT3 regulates mitochondrial fatty-acid oxidation by reversible enzyme deacetylation.” Nature 464, no. 7285 (March 4, 2010): 121–25. https://doi.org/10.1038/nature08778.

Shimazu, Tadahiro, Matthew D. Hirschey, Jing-Yi Huang, Linh T. Y. Ho, and Eric Verdin. “Acetate metabolism and aging: An emerging connection.” Mech Ageing Dev 131, no. 7–8 (2010): 511–16. https://doi.org/10.1016/j.mad.2010.05.001.

Hirschey, Matthew D., Tadahiro Shimazu, Jing-Yi Huang, and Eric Verdin. “Acetylation of mitochondrial proteins.” Methods Enzymol 457 (2009): 137–47. https://doi.org/10.1016/S0076-6879(09)05008-3.

Lombard, David B., Frederick W. Alt, Hwei-Ling Cheng, Jakob Bunkenborg, Ryan S. Streeper, Raul Mostoslavsky, Jennifer Kim, et al. “Mammalian Sir2 homolog SIRT3 regulates global mitochondrial lysine acetylation.” Mol Cell Biol 27, no. 24 (December 2007): 8807–14. https://doi.org/10.1128/MCB.01636-07.

Hirschey, Matthew D., Yong-Jin Han, Galen D. Stucky, and Alison Butler. “Imaging Escherichia coli using functionalized core/shell CdSe/CdS quantum dots.” J Biol Inorg Chem 11, no. 5 (July 2006): 663–69. https://doi.org/10.1007/s00775-006-0116-7.

Saini, S., G. D. Rubin, and M. K. Kalra. “Preface.” Mdct A Practical Approach, January 1, 2006, V–VII. https://doi.org/10.1007/88-470-0413-6.

Nicholatos, Justin W., Saurabh V. P. Tata, Timothy M. Robinette, Adam B. Francisco, Michael Platov, Jennifer D. Yordy, Olga R. Ilkayeva, et al. “Intrinsic Mitochondrial Dynamics and Cytoskeletal Properties Underlie Aging Diversity in Dogs (Accepted).” SSRN Electronic Journal, n.d. https://doi.org/10.2139/ssrn.3155620.